workflows including MyST NB and precommit added

.github/workflows/deploy.yml

@@ -1,46 +1,32 @@
-# This file was created automatically with `myst init --gh-pages` 🪄 💚
-
 name: MyST GitHub Pages Deploy
 on:
+  pull_request:
+    branches: [main]
   push:
     # Runs on pushes targeting the default branch
     branches: [main]
-env:
-  # `BASE_URL` determines the website is served from, including CSS & JS assets
-  # You may need to change this to `BASE_URL: ''`
-  BASE_URL: /${{ github.event.repository.name }}
-
-# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
-permissions:
-  contents: read
-  pages: write
-  id-token: write
-# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
-# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
-concurrency:
-  group: "pages"
-  cancel-in-progress: false
 jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Pages
+        uses: actions/configure-pages@v5
+      - uses: prefix-dev/[email protected]    
+        with:
+          path: ./_build/html
+
   deploy:
     environment:
       name: github-pages
       url: ${{ steps.deployment.outputs.page_url }}
+    if: >-
+      github.event_name == 'push' && github.ref == format('refs/heads/{0}', github.event.repository.default_branch)
+    needs: build
+    permissions:
+      pages: write
+      id-token: write
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      - name: Setup Pages
-        uses: actions/configure-pages@v3
-      - uses: actions/setup-node@v4
-        with:
-          node-version: 18.x
-      - name: Install MyST Markdown
-        run: npm install -g mystmd
-      - name: Build HTML Assets
-        run: myst build --html
-      - name: Upload artifact
-        uses: actions/upload-pages-artifact@v1
-        with:
-          path: "./_build/html"
-      - name: Deploy to GitHub Pages
-        id: deployment
-        uses: actions/deploy-pages@v2
+      - id: deployment
+        uses: actions/deploy-pages@v4  

.pre-commit-config.yaml

@@ -2,10 +2,10 @@ repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.6.0
     hooks:
-      - id: trailing-whitespace
-      - id: end-of-file-fixer
-      - id: check-yaml
       - id: check-added-large-files
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
 
   - repo: https://github.com/kynan/nbstripout
     rev: 0.7.1

docs/.gitignore

@@ -0,0 +1,2 @@
+.ipynb_checkpoints
+_build

Hello.ipynb → docs/Hello.ipynb

@@ -1,5 +1,13 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "b8b9b503-b766-478b-8c6b-67467362029d",
+   "metadata": {},
+   "source": [
+    "# Starting document"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,

docs/conf.py

@@ -0,0 +1,99 @@
+# outline for a myst_nb project with sphinx
+# build with: sphinx-build -nW --keep-going -b html . ./_build/html
+
+# load extensions
+extensions = ["myst_nb"]
+
+# specify project details
+master_doc = "index"
+project = "GlueX N-Star"
+
+# basic build settings
+exclude_patterns = [".pixi", "_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]
+nitpicky = True
+
+## myst_nb default settings
+
+# Custom formats for reading notebook; suffix -> reader
+# nb_custom_formats = {}
+
+# Notebook level metadata key for config overrides
+# nb_metadata_key = 'mystnb'
+
+# Cell level metadata key for config overrides
+# nb_cell_metadata_key = 'mystnb'
+
+# Mapping of kernel name regex to replacement kernel name(applied before execution)
+# nb_kernel_rgx_aliases = {}
+
+# Regex that matches permitted values of eval expressions
+# nb_eval_name_regex = '^[a-zA-Z_][a-zA-Z0-9_]*$'
+
+# Execution mode for notebooks
+# nb_execution_mode = 'auto'
+
+# Path to folder for caching notebooks (default: <outdir>)
+# nb_execution_cache_path = ''
+
+# Exclude (POSIX) glob patterns for notebooks
+# nb_execution_excludepatterns = ()
+
+# Execution timeout (seconds)
+# nb_execution_timeout = 30
+
+# Use temporary folder for the execution current working directory
+# nb_execution_in_temp = False
+
+# Allow errors during execution
+# nb_execution_allow_errors = False
+
+# Raise an exception on failed execution, rather than emitting a warning
+# nb_execution_raise_on_error = False
+
+# Print traceback to stderr on execution error
+# nb_execution_show_tb = False
+
+# Merge stdout/stderr execution output streams
+# nb_merge_streams = False
+
+# The entry point for the execution output render class (in group `myst_nb.output_renderer`)
+# nb_render_plugin = 'default'
+
+# Remove code cell source
+# nb_remove_code_source = False
+
+# Remove code cell outputs
+# nb_remove_code_outputs = False
+
+# Prompt to expand hidden code cell {content|source|outputs}
+# nb_code_prompt_show = 'Show code cell {type}'
+
+# Prompt to collapse hidden code cell {content|source|outputs}
+# nb_code_prompt_hide = 'Hide code cell {type}'
+
+# Number code cell source lines
+# nb_number_source_lines = False
+
+# Overrides for the base render priority of mime types: list of (builder name, mime type, priority)
+# nb_mime_priority_overrides = ()
+
+# Behaviour for stderr output
+# nb_output_stderr = 'show'
+
+# Pygments lexer applied to stdout/stderr and text/plain outputs
+# nb_render_text_lexer = 'myst-ansi'
+
+# Pygments lexer applied to error/traceback outputs
+# nb_render_error_lexer = 'ipythontb'
+
+# Options for image outputs (class|alt|height|width|scale|align)
+# nb_render_image_options = {}
+
+# Options for figure outputs (classes|name|caption|caption_before)
+# nb_render_figure_options = {}
+
+# The format to use for text/markdown rendering
+# nb_render_markdown_format = 'commonmark'
+
+# Javascript to be loaded on pages containing ipywidgets
+# nb_ipywidgets_js = {'https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js': {'integrity': 'sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=', 'crossorigin': 'anonymous'}, 'https://cdn.jsdelivr.net/npm/@jupyter-widgets/[email protected]/dist/embed-amd.js': {'data-jupyter-widgets-cdn': 'https://cdn.jsdelivr.net/npm/', 'crossorigin': 'anonymous'}}

docs/index.md

@@ -0,0 +1,5 @@
+# MyST-NB Quickstart
+
+```{toctree}
+Hello
+```

docs/notebook1.ipynb

@@ -0,0 +1,31 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "0a91cd30",
+   "metadata": {},
+   "source": [
+    "# Jupyter Notebook"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d9736bba",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print('Hello, World!')"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

docs/notebook2.md

@@ -0,0 +1,11 @@
+---
+file_format: mystnb
+kernelspec:
+  name: python3
+---
+
+# Text-based Notebook
+
+```{code-cell}
+print("Hello, World!")
+```